Difference between revisions of "Informatics"

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'''Informatics''' is the management of information. Pathologists, unfortunately, only have abysmal tools for this job.   
'''Informatics''' is the management of information. [[Pathologist]]s, unfortunately, mostly have poor tools for this job.   


The two main information system ''[[Softpath]]'' and ''[[CoPath]]'' are pathetic and look like they are out of the early 1990s.
==Software in use at pathology departments==
===Information systems===
*[[Softpath]].
*[[CoPath]].
*[[MEDITECH]].
*[[Millennium]].
*Nexus pas.net.
*[[VANTAGE]].
 
===Dictation===
*[[Dragon]].
*[[Voicebrook]].
 
===Content management===
*[[Paradigm]].
 
===Biobanking management===
* Centraxx.
 
===Image analysis===
* Cytomine - under an  ''Apache license''.<ref>URL: [http://www.cytomine.be/ http://www.cytomine.be/]. Accessed on: 20 April 2016.</ref><ref name=pmid26755625>{{Cite journal  | last1 = Marée | first1 = R. | last2 = Rollus | first2 = L. | last3 = Stévens | first3 = B. | last4 = Hoyoux | first4 = R. | last5 = Louppe | first5 = G. | last6 = Vandaele | first6 = R. | last7 = Begon | first7 = JM. | last8 = Kainz | first8 = P. | last9 = Geurts | first9 = P. | title = Collaborative analysis of multi-gigapixel imaging data using Cytomine. | journal = Bioinformatics | volume =  | issue =  | pages =  | month = Jan | year = 2016 | doi = 10.1093/bioinformatics/btw013 | PMID = 26755625 }}</ref>
 
==Pathology wikis==
{{Main|Pathology wikis}}
*Wiki use for the dissemination of pathology knowledge is increasing.
*In the general sphere, [[Wikipedia]] is dominating and will probably continue to do so.<ref name=pmid21282098>{{Cite journal  | last1 = Heilman | first1 = JM. | last2 = Kemmann | first2 = E. | last3 = Bonert | first3 = M. | last4 = Chatterjee | first4 = A. | last5 = Ragar | first5 = B. | last6 = Beards | first6 = GM. | last7 = Iberri | first7 = DJ. | last8 = Harvey | first8 = M. | last9 = Thomas | first9 = B. | title = Wikipedia: a key tool for global public health promotion. | journal = J Med Internet Res | volume = 13 | issue = 1 | pages = e14 | month =  | year = 2011 | doi = 10.2196/jmir.1589 | PMID = 21282098 }}</ref>


==Open source==
==Open source==
Open source in pathology appears to be a long way off.  One paper,<ref name=pmid15563662>{{cite journal |author=Rubin A |title=An open pathology computer system |journal=J. Clin. Pathol. |volume=57 |issue=12 |pages=1252–3 |year=2004 |month=December |pmid=15563662 |pmc=1770514 |doi=10.1136/jcp.2004.020826 |url=}}</ref> give me a bit of hope -- though I think this is a voice in the wilderness.   
Open source in pathology appears to be some way off.  One opinion paper<ref name=pmid15563662>{{cite journal |author=Rubin A |title=An open pathology computer system |journal=J. Clin. Pathol. |volume=57 |issue=12 |pages=1252–3 |year=2004 |month=December |pmid=15563662 |pmc=1770514 |doi=10.1136/jcp.2004.020826 |url=}}</ref> addresses this issue.   


IMHO, most pathologists understand very little about computers and those that think they know something often know very very little.
The radiologists are more on the ball here, e.g. [http://www.mii.ucla.edu/opensourcepacs-download-2/ UCLA's OpenSourcePACS].<ref name=pmid17249408>{{Cite journal  | last1 = Bui | first1 = AA. | last2 = Morioka | first2 = C. | last3 = Dionisio | first3 = JD. | last4 = Johnson | first4 = DB. | last5 = Sinha | first5 = U. | last6 = Ardekani | first6 = S. | last7 = Taira | first7 = RK. | last8 = Aberle | first8 = DR. | last9 = El-Saden | first9 = S. | title = OpenSourcePACS: an extensible infrastructure for medical image management. | journal = IEEE Trans Inf Technol Biomed | volume = 11 | issue = 1 | pages = 94-109 | month = Jan | year = 2007 | doi =  | PMID = 17249408 }}</ref> 
 
A few institutions (mostly American) are coming to understand this and have formed the [http://www.opendp.org/ Open Digital Pathology Consortium (opendp.org)]. There is also an [http://openslide.org/ open slide project (openslide.org)].
 
[https://qupath.github.io/ QPath] is a open source software platform for whole slide image analysis.<ref>{{Cite journal  | last1 = Bankhead | first1 = P. | last2 = Loughrey | first2 = MB. | last3 = Fernández | first3 = JA. | last4 = Dombrowski | first4 = Y. | last5 = McArt | first5 = DG. | last6 = Dunne | first6 = PD. | last7 = McQuaid | first7 = S. | last8 = Gray | first8 = RT. | last9 = Murray | first9 = LJ. | title = QuPath: Open source software for digital pathology image analysis. | journal = Sci Rep | volume = 7 | issue = 1 | pages = 16878 | month = 12 | year = 2017 | doi = 10.1038/s41598-017-17204-5 | PMID = 29203879 }}</ref>
 
[https://medevel.com/cytomine-digital-pathology/ Cytomine] is a web-based open source image processing and analysis software.
 
[https://computationalpathologygroup.github.io/ASAP/ ASAP] is an open-source whole-slide image viewer.
 
[https://www.ilastik.org/ Ilastik - interactive learning and segmentation toolkit] is an open source tool to perform segmentation and classification of images. Currently it does not support full virtual slides.<ref>{{Cite journal  | last1 = Berg | first1 = S. | last2 = Kutra | first2 = D. | last3 = Kroeger | first3 = T. | last4 = Straehle | first4 = CN. | last5 = Kausler | first5 = BX. | last6 = Haubold | first6 = C. | last7 = Schiegg | first7 = M. | last8 = Ales | first8 = J. | last9 = Beier | first9 = T. | title = ilastik: interactive machine learning for (bio)image analysis. | journal = Nat Methods | volume =  | issue =  | pages =  | month = Sep | year = 2019 | doi = 10.1038/s41592-019-0582-9 | PMID = 31570887 }}</ref>
 
==Health informatics directory==
*The University of Freiburg put together a list in 2010.<ref>URL: [http://hiww.org/ca.html
http://hiww.org/ca.html]. Accessed on: November 8, 2014.</ref>
 
==See also==
*[[Quality]].
*[[Digital pathology]].
*[[Journal of Pathology Informatics]].


==References==
==References==
{{reflist|1}}
{{reflist|2}}
 
==External links==
*[http://pathologyinformatics.org/ Association of Pathology Informatics (pathologyinformatics.org)].


[[Category:Informatics]]
[[Category:Informatics]]

Latest revision as of 09:34, 18 October 2019

Informatics is the management of information. Pathologists, unfortunately, mostly have poor tools for this job.

Software in use at pathology departments

Information systems

Dictation

Content management

Biobanking management

  • Centraxx.

Image analysis

  • Cytomine - under an Apache license.[1][2]

Pathology wikis

Main article: Pathology wikis
  • Wiki use for the dissemination of pathology knowledge is increasing.
  • In the general sphere, Wikipedia is dominating and will probably continue to do so.[3]

Open source

Open source in pathology appears to be some way off. One opinion paper[4] addresses this issue.

The radiologists are more on the ball here, e.g. UCLA's OpenSourcePACS.[5]

A few institutions (mostly American) are coming to understand this and have formed the Open Digital Pathology Consortium (opendp.org). There is also an open slide project (openslide.org).

QPath is a open source software platform for whole slide image analysis.[6]

Cytomine is a web-based open source image processing and analysis software.

ASAP is an open-source whole-slide image viewer.

Ilastik - interactive learning and segmentation toolkit is an open source tool to perform segmentation and classification of images. Currently it does not support full virtual slides.[7]

Health informatics directory

  • The University of Freiburg put together a list in 2010.[8]

See also

References

  1. ↑ URL: http://www.cytomine.be/. Accessed on: 20 April 2016.
  2. ↑ Marée, R.; Rollus, L.; Stévens, B.; Hoyoux, R.; Louppe, G.; Vandaele, R.; Begon, JM.; Kainz, P. et al. (Jan 2016). "Collaborative analysis of multi-gigapixel imaging data using Cytomine.". Bioinformatics. doi:10.1093/bioinformatics/btw013. PMID 26755625.
  3. ↑ Heilman, JM.; Kemmann, E.; Bonert, M.; Chatterjee, A.; Ragar, B.; Beards, GM.; Iberri, DJ.; Harvey, M. et al. (2011). "Wikipedia: a key tool for global public health promotion.". J Med Internet Res 13 (1): e14. doi:10.2196/jmir.1589. PMID 21282098.
  4. ↑ Rubin A (December 2004). "An open pathology computer system". J. Clin. Pathol. 57 (12): 1252–3. doi:10.1136/jcp.2004.020826. PMC 1770514. PMID 15563662. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1770514/.
  5. ↑ Bui, AA.; Morioka, C.; Dionisio, JD.; Johnson, DB.; Sinha, U.; Ardekani, S.; Taira, RK.; Aberle, DR. et al. (Jan 2007). "OpenSourcePACS: an extensible infrastructure for medical image management.". IEEE Trans Inf Technol Biomed 11 (1): 94-109. PMID 17249408.
  6. ↑ Bankhead, P.; Loughrey, MB.; Fernández, JA.; Dombrowski, Y.; McArt, DG.; Dunne, PD.; McQuaid, S.; Gray, RT. et al. (12 2017). "QuPath: Open source software for digital pathology image analysis.". Sci Rep 7 (1): 16878. doi:10.1038/s41598-017-17204-5. PMID 29203879.
  7. ↑ Berg, S.; Kutra, D.; Kroeger, T.; Straehle, CN.; Kausler, BX.; Haubold, C.; Schiegg, M.; Ales, J. et al. (Sep 2019). "ilastik: interactive machine learning for (bio)image analysis.". Nat Methods. doi:10.1038/s41592-019-0582-9. PMID 31570887.
  8. ↑ URL: [http://hiww.org/ca.html http://hiww.org/ca.html]. Accessed on: November 8, 2014.

External links

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